data_7XM9 # _model_server_result.job_id '_BpxI0UW4qe7-RzvwWCDoQ' _model_server_result.datetime_utc '2024-11-23 09:52:27' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 7xm9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":2303}' # _entry.id 7XM9 # _exptl.entry_id 7XM9 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 717.996 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate' _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 7XM9 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7XM9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation ? _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id H _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 4 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 D 1 NAG D 1 NAG 4 n D NAG 2 D 2 NAG D 2 NAG 4 n E NAG 1 E 1 NAG E 1 NAG 4 n E NAG 2 E 2 NAG E 2 NAG # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_seq_id _struct_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order disulf ? disulf1 A SG CYS 315 A CYS 315 1_555 A SG CYS 330 A CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? disulf ? disulf2 A SG CYS 884 A CYS 895 1_555 C SG CYS 55 C CYS 55 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.813 ? disulf ? disulf3 A SG CYS 886 A CYS 897 1_555 A SG CYS 892 A CYS 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf4 A SG CYS 924 A CYS 935 1_555 A SG CYS 933 A CYS 944 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 A SG CYS 1339 A CYS 1350 1_555 A SG CYS 1359 A CYS 1370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 A SG CYS 1704 A CYS 1715 1_555 A SG CYS 1719 A CYS 1730 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 B SG CYS 21 B CYS 21 1_555 B SG CYS 43 B CYS 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? disulf ? disulf8 B SG CYS 40 B CYS 40 1_555 B SG CYS 121 B CYS 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 C SG CYS 50 C CYS 50 1_555 C SG CYS 127 C CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.583 ? disulf ? disulf10 C SG CYS 72 C CYS 72 1_555 C SG CYS 75 C CYS 75 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? covale ? covale1 A ND2 ASN 1341 A ASN 1352 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale2 A ND2 ASN 1355 A ASN 1366 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 1364 A ASN 1375 1_555 F C1 NAG . A NAG 2301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale4 B ND2 ASN 93 B ASN 93 1_555 I C1 NAG . B NAG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale5 B ND2 ASN 110 B ASN 110 1_555 J C1 NAG . B NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale6 B ND2 ASN 114 B ASN 114 1_555 K C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale7 B ND2 ASN 135 B ASN 135 1_555 L C1 NAG . B NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale8 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale9 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? # _chem_comp.formula 'C39 H76 N O8 P' _chem_comp.formula_weight 717.996 _chem_comp.id 6OU _chem_comp.mon_nstd_flag . _chem_comp.name '[(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag C48 C47 6OU sing 1 n n C48 C49 6OU sing 2 n n C47 C46 6OU sing 3 n n C41 C40 6OU doub 4 z n C41 C42 6OU sing 5 n n C40 C39 6OU sing 6 n n C27 C28 6OU sing 7 n n C27 O26 6OU sing 8 n n C28 N29 6OU sing 9 n n C01 C02 6OU sing 10 n n C42 C43 6OU sing 11 n n C02 C03 6OU sing 12 n n C45 C46 6OU sing 13 n n C45 C44 6OU sing 14 n n C39 C38 6OU sing 15 n n C33 C34 6OU sing 16 n n C33 C31 6OU sing 17 n n C44 C43 6OU sing 18 n n O26 P23 6OU sing 19 n n O24 P23 6OU doub 20 n n C35 C34 6OU sing 21 n n C35 C36 6OU sing 22 n n C38 C37 6OU sing 23 n n C36 C37 6OU sing 24 n n C31 O30 6OU sing 25 n n C31 O32 6OU doub 26 n n O22 P23 6OU sing 27 n n O22 C21 6OU sing 28 n n O30 C20 6OU sing 29 n n P23 O25 6OU sing 30 n n C03 C04 6OU sing 31 n n C04 C05 6OU sing 32 n n C19 C20 6OU sing 33 n n C19 O18 6OU sing 34 n n C21 C20 6OU sing 35 n n C15 C14 6OU sing 36 n n C15 C16 6OU sing 37 n n O18 C16 6OU sing 38 n n C14 C13 6OU sing 39 n n C05 C06 6OU sing 40 n n C16 O17 6OU doub 41 n n C06 C07 6OU sing 42 n n C11 C10 6OU sing 43 n n C11 C12 6OU sing 44 n n C13 C12 6OU sing 45 n n C10 C09 6OU sing 46 n n C07 C08 6OU sing 47 n n C09 C08 6OU sing 48 n n C01 H1 6OU sing 49 n n C01 H2 6OU sing 50 n n C01 H3 6OU sing 51 n n C02 H4 6OU sing 52 n n C02 H5 6OU sing 53 n n C03 H6 6OU sing 54 n n C03 H7 6OU sing 55 n n C04 H8 6OU sing 56 n n C04 H9 6OU sing 57 n n C05 H10 6OU sing 58 n n C05 H11 6OU sing 59 n n C06 H12 6OU sing 60 n n C06 H13 6OU sing 61 n n C07 H14 6OU sing 62 n n C07 H15 6OU sing 63 n n C08 H16 6OU sing 64 n n C08 H17 6OU sing 65 n n C09 H18 6OU sing 66 n n C09 H19 6OU sing 67 n n C10 H20 6OU sing 68 n n C10 H21 6OU sing 69 n n C11 H22 6OU sing 70 n n C11 H23 6OU sing 71 n n C12 H24 6OU sing 72 n n C12 H25 6OU sing 73 n n C13 H26 6OU sing 74 n n C13 H27 6OU sing 75 n n C14 H28 6OU sing 76 n n C14 H29 6OU sing 77 n n C15 H30 6OU sing 78 n n C15 H31 6OU sing 79 n n C19 H32 6OU sing 80 n n C19 H33 6OU sing 81 n n C20 H34 6OU sing 82 n n C21 H35 6OU sing 83 n n C21 H36 6OU sing 84 n n O25 H37 6OU sing 85 n n C27 H38 6OU sing 86 n n C27 H39 6OU sing 87 n n C28 H40 6OU sing 88 n n C28 H41 6OU sing 89 n n N29 H42 6OU sing 90 n n N29 H43 6OU sing 91 n n C33 H45 6OU sing 92 n n C33 H46 6OU sing 93 n n C34 H47 6OU sing 94 n n C34 H48 6OU sing 95 n n C35 H49 6OU sing 96 n n C35 H50 6OU sing 97 n n C36 H51 6OU sing 98 n n C36 H52 6OU sing 99 n n C37 H53 6OU sing 100 n n C37 H54 6OU sing 101 n n C38 H55 6OU sing 102 n n C38 H56 6OU sing 103 n n C39 H57 6OU sing 104 n n C39 H58 6OU sing 105 n n C40 H59 6OU sing 106 n n C41 H60 6OU sing 107 n n C42 H61 6OU sing 108 n n C42 H62 6OU sing 109 n n C43 H63 6OU sing 110 n n C43 H64 6OU sing 111 n n C44 H65 6OU sing 112 n n C44 H66 6OU sing 113 n n C45 H67 6OU sing 114 n n C45 H68 6OU sing 115 n n C46 H69 6OU sing 116 n n C46 H70 6OU sing 117 n n C47 H71 6OU sing 118 n n C47 H72 6OU sing 119 n n C48 H73 6OU sing 120 n n C48 H74 6OU sing 121 n n C49 H75 6OU sing 122 n n C49 H76 6OU sing 123 n n C49 H77 6OU sing 124 n n # _atom_sites.entry_id 7XM9 _atom_sites.fract_transf_matrix[1][1] 1 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 1 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 1 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code F 5 NAG A 1 2301 2005 NAG NAG . G 6 G2E A 1 2302 2101 G2E LIG . H 7 6OU A 1 2303 2201 6OU 6OU . I 5 NAG B 1 501 301 NAG NAG . J 5 NAG B 1 502 302 NAG NAG . K 5 NAG B 1 503 303 NAG NAG . L 5 NAG B 1 504 304 NAG NAG . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 C C01 6OU . . . H 7 113.662 138.362 136.634 1 20 ? C01 6OU 2303 A 1 HETATM 2 C C02 6OU . . . H 7 114.217 139.167 135.465 1 20 ? C02 6OU 2303 A 1 HETATM 3 C C03 6OU . . . H 7 113.322 138.924 134.261 1 20 ? C03 6OU 2303 A 1 HETATM 4 C C04 6OU . . . H 7 112.896 137.464 134.276 1 20 ? C04 6OU 2303 A 1 HETATM 5 C C05 6OU . . . H 7 111.758 137.254 133.288 1 20 ? C05 6OU 2303 A 1 HETATM 6 C C06 6OU . . . H 7 110.778 138.418 133.363 1 20 ? C06 6OU 2303 A 1 HETATM 7 C C07 6OU . . . H 7 109.363 137.861 133.283 1 20 ? C07 6OU 2303 A 1 HETATM 8 C C08 6OU . . . H 7 108.565 138.646 132.254 1 20 ? C08 6OU 2303 A 1 HETATM 9 C C09 6OU . . . H 7 107.121 138.182 132.326 1 20 ? C09 6OU 2303 A 1 HETATM 10 C C10 6OU . . . H 7 106.519 138.213 130.929 1 20 ? C10 6OU 2303 A 1 HETATM 11 C C11 6OU . . . H 7 105.19 137.469 130.947 1 20 ? C11 6OU 2303 A 1 HETATM 12 C C12 6OU . . . H 7 104.884 137 129.535 1 20 ? C12 6OU 2303 A 1 HETATM 13 C C13 6OU . . . H 7 103.387 137.072 129.283 1 20 ? C13 6OU 2303 A 1 HETATM 14 C C14 6OU . . . H 7 103.097 136.345 127.981 1 20 ? C14 6OU 2303 A 1 HETATM 15 C C15 6OU . . . H 7 103.099 137.367 126.855 1 20 ? C15 6OU 2303 A 1 HETATM 16 C C16 6OU . . . H 7 103.632 136.71 125.588 1 20 ? C16 6OU 2303 A 1 HETATM 17 O O17 6OU . . . H 7 103.839 135.547 125.577 1 20 ? O17 6OU 2303 A 1 HETATM 18 O O18 6OU . . . H 7 103.873 137.469 124.444 1 20 ? O18 6OU 2303 A 1 HETATM 19 C C19 6OU . . . H 7 105.069 137.148 123.815 1 20 ? C19 6OU 2303 A 1 HETATM 20 C C20 6OU . . . H 7 105.837 138.441 123.616 1 20 ? C20 6OU 2303 A 1 HETATM 21 C C21 6OU . . . H 7 105.703 138.843 122.144 1 20 ? C21 6OU 2303 A 1 HETATM 22 O O22 6OU . . . H 7 106.937 139.094 121.541 1 20 ? O22 6OU 2303 A 1 HETATM 23 P P23 6OU . . . H 7 107.194 140.561 120.854 1 20 ? P23 6OU 2303 A 1 HETATM 24 O O24 6OU . . . H 7 106.302 140.724 119.65 1 20 ? O24 6OU 2303 A 1 HETATM 25 O O25 6OU . . . H 7 106.897 141.636 121.864 1 20 -1 O25 6OU 2303 A 1 HETATM 26 O O26 6OU . . . H 7 108.777 140.666 120.427 1 20 ? O26 6OU 2303 A 1 HETATM 27 C C27 6OU . . . H 7 109.188 140.065 119.238 1 20 ? C27 6OU 2303 A 1 HETATM 28 C C28 6OU . . . H 7 110.497 140.707 118.802 1 20 ? C28 6OU 2303 A 1 HETATM 29 N N29 6OU . . . H 7 110.814 140.277 117.454 1 20 ? N29 6OU 2303 A 1 HETATM 30 O O30 6OU . . . H 7 107.16 138.23 124.018 1 20 ? O30 6OU 2303 A 1 HETATM 31 C C31 6OU . . . H 7 107.336 138.098 125.396 1 20 ? C31 6OU 2303 A 1 HETATM 32 O O32 6OU . . . H 7 106.747 138.791 126.137 1 20 ? O32 6OU 2303 A 1 HETATM 33 C C33 6OU . . . H 7 108.296 137.062 125.952 1 20 ? C33 6OU 2303 A 1 HETATM 34 C C34 6OU . . . H 7 108.408 137.224 127.456 1 20 ? C34 6OU 2303 A 1 HETATM 35 C C35 6OU . . . H 7 108.617 135.841 128.052 1 20 ? C35 6OU 2303 A 1 HETATM 36 C C36 6OU . . . H 7 109.888 135.845 128.887 1 20 ? C36 6OU 2303 A 1 HETATM 37 C C37 6OU . . . H 7 109.846 134.7 129.884 1 20 ? C37 6OU 2303 A 1 HETATM 38 C C38 6OU . . . H 7 111.268 134.338 130.28 1 20 ? C38 6OU 2303 A 1 HETATM 39 C C39 6OU . . . H 7 111.271 133.997 131.759 1 20 ? C39 6OU 2303 A 1 HETATM 40 C C40 6OU . . . H 7 112.328 132.936 132.022 1 20 ? C40 6OU 2303 A 1 HETATM 41 C C41 6OU . . . H 7 112.101 132.009 132.925 1 20 ? C41 6OU 2303 A 1 HETATM 42 C C42 6OU . . . H 7 113.154 130.94 133.194 1 20 ? C42 6OU 2303 A 1 HETATM 43 C C43 6OU . . . H 7 112.589 129.922 134.18 1 20 ? C43 6OU 2303 A 1 HETATM 44 C C44 6OU . . . H 7 113.475 129.879 135.422 1 20 ? C44 6OU 2303 A 1 HETATM 45 C C45 6OU . . . H 7 112.591 129.69 136.65 1 20 ? C45 6OU 2303 A 1 HETATM 46 C C46 6OU . . . H 7 112.183 131.054 137.201 1 20 ? C46 6OU 2303 A 1 HETATM 47 C C47 6OU . . . H 7 111.244 130.856 138.388 1 20 ? C47 6OU 2303 A 1 HETATM 48 C C48 6OU . . . H 7 109.832 131.325 138.033 1 20 ? C48 6OU 2303 A 1 HETATM 49 C C49 6OU . . . H 7 109.017 131.516 139.313 1 20 ? C49 6OU 2303 A 1 # _model_server_stats.io_time_ms 59 _model_server_stats.parse_time_ms 33 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 49 #